Cute and cuddly is one thing, but a bawling Marill is too much even for Misty. When all Misty's attempts to toughen up the picayune Pokémon fall short, Team Rocket takes her by surprise. Misty is left with no help or hope in sight, save for little Marill.
Brock looks through his guidebook and informs Ash that they should head to Azalea Town for the next Gym. The trio soon stops to admire a scenic lakeside town, where Brock spots a girl at a cliff. Misty also spots a Marill and attempts to catch it. However, the Poké Ball simply hits Marill on the head, causing it to cry out loud. As Brock comforts the Marill. Ash notices the pink bow on her tail and points out that she must already have a Trainer. Misty tries to hold her, but Marill doesn't seem to like her and cries again.
Team Rocket appears, disguised as farmers, and they offer to give the group a lift. Unaware of the plot, Ash and his friends hop on the vehicle. Just then, two hands appear from the hay and grab hold of Pikachu and Marill. Team Rocket detaches the vehicle's tray and flees, leaving Ash, Misty, and Brock behind. Ash and his friends give chase as Team Rocket recites their motto. Marill lets out an ear-splitting cry, causing Meowth to lose control of the truck and crashes it into a railing, sending Team Rocket blasting off. Pikachu and Marill roll down the hill towards the riverside. Ash tries to go after them but lands on a tree. Brock stays behind and keeps Togepi safe, while Misty continues down the hill and grabs the two Pokémon. Unfortunately, she is unable to stop and falls into the river. Ash and Brock watch as Misty, with Pikachu and Marill in hand, is washed downstream.
The girl Brock was gazing at before suddenly rushes towards him and Ash. She grabs Ash by the shirt and begins shaking him violently, demanding to know where her Marill is. Brock is instantly lovestruck, and introduces himself to her. She replies that her name is Wilhomena. Elsewhere, Misty, Pikachu, and Marill wash ashore as Marill begins to cry again. An enraged Misty yells at Marill, causing her to try to run off and inadvertently leave her pink ribbon behind. Misty tries to hold Marill, but it simply refuses to be with her. After calming down, Misty suggests that Marill use its sensitive ears to find its Trainer. During the search, Misty gets impatient with Marill's crying. Later on, Ash, Brock, and Wilhomena happen upon the riverside and Togepi spots Marill's pink ribbon.
Meanwhile, Marill rushes off after spotting a Butterfree, and follows it to a flower meadow. Marill begins to launch several Water Gun attacks at the Butterfree, but inadvertently stirs up a swarm of Beedrill. Ash, Brock, and Wilhomena hear Pikachu screaming and run towards the sound, but they miss Misty, Pikachu, and Marill. The situation becomes more critical as Misty, Pikachu, and Marill reach a dead end. Thinking quickly, Misty tells Pikachu to use Thunder Shock, which scares off the Beedrill. Afterwards, rain begins to fall, prompting Misty and the two Pokémon to find shelter in a tree hollow, while Ash, Wilhomena, and Brock seek refuge under some trees. The lightning starts scaring Marill, who rushes out of the tree crying, and Misty and Pikachu follow her. Lightning strikes a nearby tree, but Misty grabs Marill just in time to save her. Misty is about to scold Marill for running off again, but realizes that she is relieved to see her safe.
Later, while Misty and the two Pokémon cross a rope bridge, a mechanical hand appears from the trees and begins shaking it. Team Rocket reappears in their Meowth balloon and grabs the two Pokémon. Misty leaps and manages to grab a hold of Marill. With Misty's added weight, Meowth is forced to let go of the claw, sending Misty and Marill into the ravine below. However, Ash's Chikorita uses its vines to save them, and she pulls the pair up to where Ash, Brock, and Wilhomena are standing. Ash then has Chikorita launch a Razor Leaf at Team Rocket's balloon. The attack strikes, and the balloon crashes next to Ash and his friends. Pikachu is released and returns to Ash. Jessie and Jamesbattle Ash and Misty with Arbok and Weezing. Misty calls on Poliwag and it repels Weezing's Sludge. Then, Arbok's Poison Sting almost hits Misty, but Marill uses Water Gun to save her. After that, Pikachu blasts Team Rocket off with Thunderbolt.
After reuniting with Marill, Wilhomena is glad to see that she has made some new friends. Ash congratulates Pikachu's efforts, but Chikorita interjects and receives most of the praise. Wilhomena offers the group a place to stay at her lake house, but Ash is eager to reach Azalea Town and declines. She thanks the group before driving off in a limousine, leaving both Misty and Brock heartbroken.
There is a repeating scene (seen in the trees) when James says "Yeah, how do you like the sound of them apples..."
When Beedrill appear, they can be heard saying their Japanese name, Spear.
In the scene where Misty, Pikachu and Marill are hiding inside of the tree, Misty's shirt appears white and her straps are black. They remain this way until Team Rocket attacks her on the bridge. (This is most likely due to lighting effects from the storm as her shirt is seen to have a little color still.)
When Team Rocket send out Arbok and Weezing, an extra Poké Ball sound effect plays as they throw the Poké Balls, before the sound effect accompanying the Pokémon actually appearing is heard.